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The structure of human Siderocalin bound to the bacterial siderophore 2,3-DHBA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L6M PDB ENTRY 1L6M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 289 HosaA.18070.a at 10mg/ml. 1.3M Ammonium sulfate, 0.2M Lithium sulfate, 50mM sodium chloride, 0.1M sodium acetate, pH 4.5. Cryo protection 15% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 4.55 72.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.476 α = 90 b = 116.452 β = 90 c = 120.194 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210 2011-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.5 50 98.5 0.118 12.8 6.2 55324
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.54 99.7 0.479 6.2 2757
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1L6M 2.51 42.01 55279 5498 97.17 0.251 0.2469 0.2637 0.2882 0.3041 RANDOM 41.7926
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 3.58 3.6 -7.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.937 r_dihedral_angle_4_deg 22.821 r_dihedral_angle_3_deg 16.649 r_dihedral_angle_1_deg 6.871 r_angle_refined_deg 1.481 r_angle_other_deg 0.957 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.937 r_dihedral_angle_4_deg 22.821 r_dihedral_angle_3_deg 16.649 r_dihedral_angle_1_deg 6.871 r_angle_refined_deg 1.481 r_angle_other_deg 0.957 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5550 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 139
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling